No abstract

As genome sequencing outstrips the rate of high-quality, lowthroughput biochemical and genetic experimentation, accurate annotation of protein function becomes a bottleneck in the progress of the biomolecular sciences. Most gene products are now annotated by homology, in which an experimentally determined function is applied to a similar sequence. This procedure becomes error-prone between more divergent sequences and can contaminate biomolecular databases. Here, we propose a computational method of assignment of function, termed Generalized Functional Linkages (GFL), that combines nonhomology-based methods with other types of data. Functional linkages describe pairwise relationships between proteins that work together to perform a biological task. GFL provides a Bayesian framework that improves annotation by arbitrating a competition among biological process annotations to best describe the target protein. GFL addresses the unequal strengths of functional linkages among proteins, the quality of existing annotations, and the similarity among them while incorporating available knowledge about the cellular location or individual molecular function of the target protein. We demonstrate GFL with functional linkages defined by an algorithm known as zorch that quantifies connectivity in protein-protein interaction networks. Even when using proteins linked only by indirect or high-throughput interactions, GFL predicts the biological processes of many proteins in Saccharomyces cerevisiae, improving the accuracy of annotation by 20% over majority voting.Gene Ontology ͉ protein annotation ͉ protein function ͉ protein-protein interactions ͉ zorch

Fruitspotting bugs, Amblypelta nitida Stål, and A. lutescens lutescens Distant (Hemiptera: Coreidae), are polyphagous, native Australian pests of a wide range of tropical and subtropical fruit and nut crops. Both species occur predominantly along Australia's eastern coastline, A. nitida from c. 17°S-35°S and A. l. lutescens from c. 11°S-27°S, and as such, they are distributed across some of Australia's most important horticultural regions. Adults are cryptic and highly mobile, making population monitoring within affected tree crops difficult. Nymphs and adults inject salivary sucrase into plant tissue while feeding; this causes significant damage to fruiting structures and often renders them unsaleable. Despite their economic importance, many aspects of fruitspotting bug biology and ecology remain understudied; their chemical ecology, host-plant relationships, movements into, out of and within crops, and interactions with natural enemies are poorly understood. Currently, control of both species relies on applications of synthetic broad-spectrum insecticides, and the recent withdrawal of endosulfan has resulted in an increased use of more disruptive compounds. This paper reviews current knowledge of fruitspotting bug biology and ecology, and the strategies that are currently employed for control. Importantly, a synthetic lure based on some of the volatile compounds emitted by male A. l. lutescens has recently been developed and incorporated into a prototype trap. The device offers a promising new approach to population monitoring and the development of integrated management strategies for this species. Areas of research critical to the development of sustainable management strategies for fruitspotting bugs include: (1) host-plant relationships between fruitspotting bugs and their crop and non-crop host plants;(2) fruitspotting bug dispersal behaviour and movement patterns between and within crops, and between crops and non-crop vegetation; (3) methods for implementing biological control strategies; (4) utilising pheromone traps for monitoring and capture of fruitspotting bugs; and (5) screening of selective insecticides.

Fruitspotting bugs (FSB) Amblypelta nitida Stål and Amblypelta lutescens lutescens (Distant) (Hemiptera: Coreidae) are major native pests in subtropical and tropical horticultural crops in Australia and a key pest in avocado. The pest is known to cause significant damage to more than 25 different tree fruit and nut crops and some vine fruits through the coastal and subcoastal areas of Queensland, northern New South Wales, the Northern Territory and northwestern Western Australia. Current management is repeated applications of broad-spectrum insecticides, which is not sustainable in the long-term. This study, commenced in March 2011, is investigating an integrated approach including the following components: 1. Chemical control: A number of insecticides have been evaluated in laboratory and field trials. We are working towards availability of new chemicals for farmers. 2. Cultural control: Susceptibility of different cultivars and planting densities are investigated 3. Monitoring: Monitoring of FSB has been a challenge, but is crucial to strategic management. Two different monitoring tools have been investigated. i)Trap crops: Investigation of small hedges of highly attractive host plants as a monitoring tool. A technique and monitoring protocol for A. nitida has now been developed. ii) Pheromone traps: Pheromones have been investigated for both Amblypelta spp. A use pattern and a prototype of trap for A.l. lutescens have been developed and commercialisation of the trap is underway. 4. Biological control: Different natural enemies of FSB have been investigated including three species of FSB egg parasitoids to improve our understanding of their biology and ecology. Their biocontrol potential is being evaluated in small scale trials. 5. Area Wide Management (AWM): In order to allow management beyond farm level an area wide scale strategy is being developed and trialled with a pilot group of farmers. This study is finishing in April 2016 and outcomes of different components to date and long-term benefits to industries involved will be presented.